Just to be sure. I would like to check that I am doing the right thing with powering. I think I what to use a 3 cell LIPO which delivers between 11.1v and about 12.3v during it's discharge cycle. If I connect the battery to the power leads of the shield and have the power jumper set then the arduino will get power from the battery as well? Also when it is hooked up this way can I safely connect the USB cable and upload firmware.

This will probably work if you don't have too much extra drain on the Arduino 5v supply. The Arduino is rated for 7-12v input. At the higher end of that range, the linear voltage regulator will be working pretty hard.

The other consideration is the effect of of motor noise and power spikes on the Arduino. In general we recommend separate supplies to minimize these effects.

Oh dahm,Well what if I split the power at the battery and send one lead to the arduino and one to the shield? They are still pulling off the same supply but the shield and the brain would be separate. Also: should I then plug the arduino in by the power plug that I got a nine volt battery for with the beginner package? (not the 5V in)